[gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

[Christopher Neale]

How long are your simulations? I build a DPPC bilayer with charmm-GUI and simulate for 300 ns at 323 K and the APL has a mean of 0.61 nm^2 and a standard deviation of 0.01 nm^2. However, the APL does happen to dip down to 0.59 within 10 ns... it's just that the fluctuations will also sometimes take it as high as 0.65 and as low as 0.57. Maybe give us your simulation time and upload a plot of APL vs. time and post the link here (no direct attachments please). If you're running 10-20 ns and you see the APL get low then you may simply need to run for longer.

Here is the data from my simulation of DPPC at 323K:
https://www.dropbox.com/s/adu4ft8dhuyc9c2/dppc_323k_apl.pdf?dl=0

I suggest you figure things out with DPPC before moving on to your PA lipids.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nidhin Thomas <nidhin.thomas0624 at gmail.com>
Sent: 13 June 2016 19:32:47
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

Hello everyone,

I have also given below the map file that I have used for equilibration.

integrator = md
dt = 0.002
nsteps = 2000000
nstlog = 1000
nstxout = 5000
nstvout = 1000
nstfout = 1000
nstcalcenergy = 100
nstxtcout       = 1000
nstenergy = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
tcoupl = Nose-Hoover
tc_grps = MEMB SOL_ION
tau_t = 1.0 1.0
ref_t = 323.15 323.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = MEMB SOL_ION
;
refcoord_scaling = com


Thanks,

Nidhin Thomas
University of Houston

> Message: 4
> Date: Mon, 13 Jun 2016 17:51:43 +0000
> From: Christopher Neale <chris.neale at alum.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>       <gromacs.org_gmx-users at maillist.sys.kth.se>, "gmx-users at gromacs.org"
>       <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer
>       obtained        from CHARMM-GUI
> Message-ID:
>       <SN2PR03MB23010A1EA13D95F4EC7877C1C5530 at SN2PR03MB2301.namprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="Windows-1252"
>
> In future posts, it is best to copy and paste your .mdp file because we can not all get attachments from the list.
>
> Regarding your results, it is my understanding that the CHARMM-GUI has parameters for, and can build, many lipids systems whose parameters have not been completely validated by simulations in the literature (e.g. for things like APL). Last time I looked, PG was the only anionic charmm36 lipid that was shown to behave properly in bilayers (Klauda), though others may have since been shown to work well.
>
> If the issue is not simply that the PA parameters are not very good, then one likely source of problem is that perhaps you are not using the NBfix ions? That could be a big deal. I never use Na with membranes for this reason, so you could try KCl instead.
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nidhin Thomas <nidhin.thomas0624 at gmail.com>
> Sent: 12 June 2016 18:38:43
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained        from CHARMM-GUI
>
> Hello GROMACS Users,
>
> I have modelled a mixed bilayer system consisting of 35 DPPC lipids and one POPA lipid (in each monolayers) using CHARMM-GUI. NPT ensemble was chosen while creating the model. TIP3 water model was used for modeling. I did not use surface tension for the membrane.
>
> I have simulated the system for 50 nanoseconds now. I have noticed that average area per lipid of the system is only 58.55 Angstrom2. I saw from literature that it should be around 63 and even at CHARMM-GUI, it is mentioned as 63 while creating the bilayer.
>
> I have used the exact .mdp files given by CHARMM-GUI for minimization, equilibration and production run.
>
> Can anyone please help me identify what could have possibly gone wrong in my simulation? I have attached the .mdp file used for production run and equilibration here for reference.
>
> In addition, I keep on getting these NOTES while running the grompp command prior to mdrun before it creates a .tpr file. I don?t know if this has got something to do with the simulation.
>
> NOTE 1 [file step7_production_2.mdp]:
>  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
> Estimate for the relative computational load of the PME mesh part: 0.05
> Excluding 2 bonded neighbours molecule type 'TIP3'
>
> There was 1 note
> Excluding 1 bonded neighbours molecule type 'POT'
> Removing all charge groups because cutoff-scheme=Verlet
> Setting the LD random seed to 2417118902
> Estimate for the relative computational load of the PME mesh part: 0.05
>
> There was 1 note
> Removing all charge groups because cutoff-scheme=Verlet
>
> Thanks a lot for the help!
>
> Nidhin Thomas
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